Low-Complexity Joint Channel Estimation and List Decoding of Short Codes

A pilot-assisted transmission (PAT) scheme is proposed for short blocklengths, where the pilots are used only to derive an initial channel estimate for the list construction step. The final decision of the message is obtained by applying a non-coherent decoding metric to the codewords composing the list. This allows one to use very few pilots, thus reducing the channel estimation overhead. The method is applied to an ordered statistics decoder for communication over a Rayleigh block-fading channel. Gains of up to $1.2$ dB as compared to traditional PAT schemes are demonstrated for short codes with QPSK signaling. The approach can be generalized to other list decoders, e.g., to list decoding of polar codes.Comment: Accepted at the 12th International ITG Conference on Systems, Communications and Coding (SCC 2019), Rostock, German

A STUDY OF LINEAR ERROR CORRECTING CODES

Since Shannon's ground-breaking work in 1948, there have been two main development streams of channel coding in approaching the limit of communication channels, namely classical coding theory which aims at designing codes with large minimum Hamming distance and probabilistic coding which places the emphasis on low complexity probabilistic decoding using long codes built from simple constituent codes. This work presents some further investigations in these two channel coding development streams. Low-density parity-check (LDPC) codes form a class of capacity-approaching codes with sparse parity-check matrix and low-complexity decoder Two novel methods of constructing algebraic binary LDPC codes are presented. These methods are based on the theory of cyclotomic cosets, idempotents and Mattson-Solomon polynomials, and are complementary to each other. The two methods generate in addition to some new cyclic iteratively decodable codes, the well-known Euclidean and projective geometry codes. Their extension to non binary fields is shown to be straightforward. These algebraic cyclic LDPC codes, for short block lengths, converge considerably well under iterative decoding. It is also shown that for some of these codes, maximum likelihood performance may be achieved by a modified belief propagation decoder which uses a different subset of 7^ codewords of the dual code for each iteration. Following a property of the revolving-door combination generator, multi-threaded minimum Hamming distance computation algorithms are developed. Using these algorithms, the previously unknown, minimum Hamming distance of the quadratic residue code for prime 199 has been evaluated. In addition, the highest minimum Hamming distance attainable by all binary cyclic codes of odd lengths from 129 to 189 has been determined, and as many as 901 new binary linear codes which have higher minimum Hamming distance than the previously considered best known linear code have been found. It is shown that by exploiting the structure of circulant matrices, the number of codewords required, to compute the minimum Hamming distance and the number of codewords of a given Hamming weight of binary double-circulant codes based on primes, may be reduced. A means of independently verifying the exhaustively computed number of codewords of a given Hamming weight of these double-circulant codes is developed and in coiyunction with this, it is proved that some published results are incorrect and the correct weight spectra are presented. Moreover, it is shown that it is possible to estimate the minimum Hamming distance of this family of prime-based double-circulant codes. It is shown that linear codes may be efficiently decoded using the incremental correlation Dorsch algorithm. By extending this algorithm, a list decoder is derived and a novel, CRC-less error detection mechanism that offers much better throughput and performance than the conventional ORG scheme is described. Using the same method it is shown that the performance of conventional CRC scheme may be considerably enhanced. Error detection is an integral part of an incremental redundancy communications system and it is shown that sequences of good error correction codes, suitable for use in incremental redundancy communications systems may be obtained using the Constructions X and XX. Examples are given and their performances presented in comparison to conventional CRC schemes

Computational design with flexible backbone sampling for protein remodeling and scaffolding of complex binding sites

Dissertation presented to obtain the Doutoramento (Ph.D.) degree in Biochemistry at the Instituto de Tecnologia Qu mica e Biol ogica da Universidade Nova de LisboaComputational protein design has achieved several milestones, including the design of a new protein fold, the design of enzymes for reactions that lack natural catalysts, and the re-engineering of protein-protein and protein-DNA binding speci city. These achievements have spurred demand to apply protein design methods to a wider array of research problems. However, the existing computational methods have largely relied on xed-backbone approaches that may limit the scope of problems that can be tackled. Here, we describe four computational protocols - side chain grafting, exible backbone remodeling, backbone grafting, and de novo sca old design - that expand the methodological protein design repertoire, three of which incorporate backbone exibility. Brie y, in the side chain grafting method, side chains of a structural motif are transplanted to a protein with a similar backbone conformation; in exible backbone remodeling, de novo segments of backbone are built and designed; in backbone grafting, structural motifs are explicitly grafted onto other proteins; and in de novo sca olding, a protein is folded and designed around a structural motif. We developed these new methods for the design of epitope-sca old vaccines in which viral neutralization epitopes of known three-dimensional structure were transplanted onto nonviral sca old proteins for conformational stabilization and immune presentation.(...

An FPGA implementation of an investigative many-core processor, Fynbos : in support of a Fortran autoparallelising software pipeline

Includes bibliographical references.In light of the power, memory, ILP, and utilisation walls facing the computing industry, this work examines the hypothetical many-core approach to finding greater compute performance and efficiency. In order to achieve greater efficiency in an environment in which Moore’s law continues but TDP has been capped, a means of deriving performance from dark and dim silicon is needed. The many-core hypothesis is one approach to exploiting these available transistors efficiently. As understood in this work, it involves trading in hardware control complexity for hundreds to thousands of parallel simple processing elements, and operating at a clock speed sufficiently low as to allow the efficiency gains of near threshold voltage operation. Performance is there- fore dependant on exploiting a new degree of fine-grained parallelism such as is currently only found in GPGPUs, but in a manner that is not as restrictive in application domain range. While removing the complex control hardware of traditional CPUs provides space for more arithmetic hardware, a basic level of control is still required. For a number of reasons this work chooses to replace this control largely with static scheduling. This pushes the burden of control primarily to the software and specifically the compiler, rather not to the programmer or to an application specific means of control simplification. An existing legacy tool chain capable of autoparallelising sequential Fortran code to the degree of parallelism necessary for many-core exists. This work implements a many-core architecture to match it. Prototyping the design on an FPGA, it is possible to examine the real world performance of the compiler-architecture system to a greater degree than simulation only would allow. Comparing theoretical peak performance and real performance in a case study application, the system is found to be more efficient than any other reviewed, but to also significantly under perform relative to current competing architectures. This failing is apportioned to taking the need for simple hardware too far, and an inability to implement static scheduling mitigating tactics due to lack of support for such in the compiler

Towards High Throughput Single Crystal Neutron Diffraction of Hydrogen Bonded Molecular Complexes

This work presents findings from experiments carried out using the neutron Laue method in tandem with laboratory source X-ray diffraction to characterise a series of organic molecular complexes which exhibit interesting, and potentially “tunable”, temperature dependent charge transfer effects, such as proton migration and proton disorder within hydrogen bonded networks. These subtle processes are studied by variable temperature neutron diffraction studies, allowing the positional and anisotropic displacement parameters of the hydrogen atoms to be refined accurately and their evolution with temperature followed. The hydrogen atom behaviour is found to be influenced by the local environment, including weak intermolecular interactions in the vicinity of the hydrogen bond under study. Complexes of urea and methyl substituted ureas with small organic acids are presented, which show robust and reproducible structural motifs. In favourable circumstances, these contain short, strong hydrogen bonds (SSHBs) within which the proton may undergo temperature dependent migration. By synthesising a number of complexes containing SSHBs, potential routes to the design of proton migration complexes are found, which utilise crystal engineering principles and pKa matching. Variable temperature studies conducted on these complexes also show unusual thermal expansion properties and phase transitions in urea-acid complexes which do not display proton migration. Systems containing hydrogen bonded dimers of 3,5-dinitrobenzoic acid are also studied, and shown to contain temperature proton disorder within moderate strength hydrogen bonds linking the dimers. The presence and potential onset temperature of any disorder is found to be influenced by interactions around the acid dimers and potential routes to controlling proton disorder are discussed. Complexes of the proton sponge, 1,8-bis(dimethylamino)napthalene (DMAN), with organic acids are also presented, in which the structures have been determined using neutron diffraction. DMAN readily accepts a proton from the acid co-molecules used in forming the complexes, forming a strong intramolecular SSHB within the protonated DMAN. Strong intermolecular hydrogen bonds are also induced between the acid molecules in many cases. The neutron studies presented here investigate the effect of weak interactions on the behaviour of hydrogen atoms located within these SSHBs, and also indicate over what distance such interactions significantly affect the hydrogen atom behaviour.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Algorithmische und Code-Optimierungen Molekulardynamiksimulationen für Verfahrenstechnik

The focus of this work lies on implementational improvements and, in particular, node-level performance optimization of the simulation software ls1-mardyn. Through data structure improvements, SIMD vectorization and, especially, OpenMP parallelization, the world’s first simulation of 2*1013 molecules at over 1 PFLOP/sec was enabled. To allow for long-range interactions, the Fast Multipole Method was introduced to ls1-mardyn. The algorithm was optimized for sequential, shared-memory, and distributed-memory execution on up to 32,768 MPI processes.Der Fokus dieser Arbeit liegt auf Code-Optimierungen und insbesondere Leistungsoptimierung auf Knoten-Ebene für die Simulationssoftware ls1-mardyn. Durch verbesserte Datenstrukturen, SIMD-Vektorisierung und vor allem OpenMP-Parallelisierung wurde die weltweit erste Petaflop-Simulation von 2*1013 Molekülen ermöglicht. Zur Simulation von langreichweitigen Wechselwirkungen wurde die Fast-Multipole-Methode in ls1-mardyn eingeführt. Sequenzielle, Shared- und Distributed-Memory-Optimierungen wurden angewandt und erlaubten eine Ausführung auf bis zu 32768 MPI-Prozessen

Computational Design of Zinc Binding Sites at Protein Interfaces and Enzyme Active Sites

Engineered proteins will continue to expand the molecular toolkit for applications in medicine, biotechnology, and basic research. While protein engineering efforts often use a parts list limited to the twenty amino acids, metal ions expand the parts list and are critical for the folding and function of 30-40% of known proteins. In particular, zinc ions are common as structural metal sites and catalytic metal sites. Thus, the work described here uses and develops computational methods to engineer structural zinc sites at protein interfaces and catalytic zinc sites at potential active sites. The first chapter discusses the design of a de novo zinc-mediated heterodimeric interaction that targets wild-type ubiquitin. Although zinc binding was successful, a lack of cooperativity resulted in a modest effect of zinc on ubiquitin binding affinity. The second chapter presents a de novo zinc-mediated homodimer as an alternative protein interface design strategy with more cooperative metal binding. Zinc binding improved the homodimer binding affinity by >100-fold, and crystal structures demonstrate moderate accuracy in the design of the zinc sites and the protein-protein interaction. The third chapter reveals the serendipitous discovery of de novo catalysis by this designed zinc-mediated homodimer. This discovery emphasizes the usefulness of protein interfaces for active site formation, the power of zinc for catalysis, and the modest rates achieved thus far in the field of de novo enzyme design. The fourth chapter introduces our efforts to purposefully design a new catalytic motif in a deeper protein cleft. Our approach differs from most enzyme design studies that instead rely on existing catalytic motifs and modify substrate-binding residues. A conformational change shown in the crystal structure of a designed zinc site in a TIM-barrel scaffold emphasizes the importance of second-shell hydrogen bonds to support the primary coordination shell for robust metal binding in deeper protein clefts. In summary, we have endeavored to better understand and more reliably engineer protein structure and function using a predictive computational approach, and as we improve our ability to design zinc sites in proteins, more sophisticated protein functions can be engineered for applied purposes.Doctor of Philosoph